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A survey of mapping algorithms in the long-reads era
Stockholm University, Faculty of Science, Department of Mathematics. Stockholm University, Science for Life Laboratory (SciLifeLab).ORCID iD: 0000-0001-7378-2320
Number of Authors: 42023 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 24, no 1, article id 133Article, review/survey (Refereed) Published
Abstract [en]

It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend framework used for short reads to a seed-and-chain framework due to the seed abundance in each read. The main novelties are based on alternative seed constructs or chaining formulations. Dozens of tools now exist, whose heuristics have evolved considerably. We provide an overview of the methods used in long-read mappers. Since they are driven by implementation-specific parameters, we develop an original visualization tool to understand the parameter settings (http:// bcazaux.polytech-lille.net/Minimap2/).

Place, publisher, year, edition, pages
2023. Vol. 24, no 1, article id 133
National Category
Environmental Biotechnology Biological Sciences
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URN: urn:nbn:se:su:diva-218376DOI: 10.1186/s13059-023-02972-3ISI: 001000395100002PubMedID: 37264447Scopus ID: 2-s2.0-85160969471OAI: oai:DiVA.org:su-218376DiVA, id: diva2:1775827
Available from: 2023-06-27 Created: 2023-06-27 Last updated: 2023-06-27Bibliographically approved

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Sahlin, Kristoffer

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